The jet was flying in formation north-east of the Wattisham Airfield in Suffolk, performing a low-level manoeuvre.
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The Civil Aviation Authority said that safety during the incident "had been much reduced".
The drone was carrying out an agricultural survey at a height of 100 meters. The pilot of the drone reported the incident, but was not required to inform Wattisham Airfield of his plans. He said that there was a high risk of collision.
Earlier, London Gatwick Airport was brought to a standstill due to two drones flying near the airport.